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1 process SHOVILL {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}shovill${params.fs}1.1.0" : null)
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6 conda (params.enable_conda ? "bioconda::shovill=1.1.0 conda-forge::pigz" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' :
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9 'quay.io/biocontainers/shovill:1.1.0--0' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path("${prefix}${params.fs}contigs.fa") , emit: contigs
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16 tuple val(meta), path("${prefix}${params.fs}shovill.corrections") , emit: corrections
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17 tuple val(meta), path("${prefix}${params.fs}shovill.log") , emit: log
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18 tuple val(meta), path("${prefix}${params.fs}{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
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19 tuple val(meta), path("${prefix}${params.fs}contigs.{fastg,gfa,LastGraph}") , emit: gfa, optional: true
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20 path "versions.yml" , emit: versions
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21
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22 when:
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23 task.ext.when == null || task.ext.when
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24
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25 script:
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26 def args = task.ext.args ?: ''
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27 def memory = (task.memory ? task.memory.toGiga() : 16)
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28 prefix = (task.ext.prefix ?: meta.id)
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29 """
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30 shovill \\
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31 --R1 ${reads[0]} \\
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32 --R2 ${reads[1]} \\
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33 $args \\
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34 --tmpdir ${prefix}${params.fs}tmp \\
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35 --cpus $task.cpus \\
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36 --ram $memory \\
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37 --outdir $prefix \\
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38 --force
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39
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40 cat <<-END_VERSIONS > versions.yml
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41 "${task.process}":
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42 shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
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43 END_VERSIONS
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44 """
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45 } |
